Contacts of the strand formed by residues 127 - 134 (chain D) in PDB entry 3ZXR
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 127 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119D LEU* 3.6 7.0 - - - +
125D ALA* 4.3 0.2 - - - +
126D ASP* 1.3 95.8 + - - +
128D ALA* 1.3 61.1 + - - +
129D TYR* 3.6 40.2 + - + +
234D SER* 3.9 17.5 - - - -
280D SER 3.9 0.3 - - - +
281D LEU* 3.4 5.2 - - - +
282D TRP* 2.9 43.3 + - - +
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Residues in contact with ALA 128 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D GLU* 6.2 2.1 - - + +
119D LEU* 3.4 13.5 - - + +
127D THR* 1.3 73.5 - - - +
129D TYR* 1.3 62.1 + - - +
130D PHE* 3.6 19.4 - - + -
234D SER* 3.3 4.1 - - - -
235D LEU* 3.1 29.7 + - + -
280D SER 3.5 4.7 - - - +
281D LEU* 3.7 18.2 - - + -
305D TYR* 5.7 0.4 - - - +
384D LEU* 3.9 14.1 - - + -
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Residues in contact with TYR 129 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D THR* 3.6 26.8 + - + +
128D ALA* 1.3 72.2 - - - +
130D PHE* 1.3 63.3 + - - +
232D PHE* 3.7 34.8 - + + -
233D ASN* 3.5 22.9 - - - -
234D SER* 3.5 11.9 - - - -
278D HIS 3.5 0.7 - - - +
279D GLN* 3.4 6.9 - - - +
280D SER* 2.9 36.9 + - - +
282D TRP* 3.4 52.6 - + + -
501D IQ1 3.7 4.4 - - - +
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Residues in contact with PHE 130 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D ALA* 3.6 24.7 - - + -
129D TYR* 1.3 78.4 - - - +
131D GLY* 1.3 59.9 + - - +
132D ALA* 4.1 1.2 + - + -
232D PHE* 3.3 4.9 - - - +
233D ASN 2.8 30.7 + - - +
235D LEU* 3.7 33.2 - - + -
238D ALA* 3.9 20.4 - - + +
277D CYS* 4.6 6.3 - - + -
278D HIS 3.4 2.7 - - - -
279D GLN* 3.7 34.5 - - + -
305D TYR* 4.4 7.4 - - - -
380D PHE* 3.5 59.0 - + + -
383D MET* 4.2 3.8 - - - -
384D LEU* 4.4 2.7 - - + -
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Residues in contact with GLY 131 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D PHE* 1.3 72.7 - - - +
132D ALA* 1.3 60.2 + - - -
230D TYR 5.6 0.4 - - - -
232D PHE* 3.7 18.6 - - - -
276D HIS 3.6 1.0 - - - +
277D CYS* 3.5 2.6 - - - -
278D HIS* 2.7 41.2 + - - +
501D IQ1 3.5 25.9 - - - +
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Residues in contact with ALA 132 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D PHE 4.1 1.5 + - - -
131D GLY* 1.3 74.5 - - - -
133D GLU* 1.3 66.6 + - - +
134D ALA 3.9 0.8 + - - -
228D ILE 5.1 1.0 - - - +
229D ASN* 4.4 6.6 + - - -
230D TYR* 4.6 21.4 + - + +
238D ALA* 6.5 0.2 - - + -
242D MET* 3.3 30.7 - - + -
275D MET* 4.4 4.7 - - + -
276D HIS 3.3 7.2 - - - +
277D CYS* 4.7 2.7 - - - +
380D PHE* 4.3 17.5 - - + -
501D IQ1 3.9 10.3 - - - +
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Residues in contact with GLU 133 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D ALA* 1.3 77.6 - - - +
134D ALA* 1.3 59.9 + - - +
135D GLU* 3.3 4.7 + - + +
227D GLU* 2.9 20.0 - - - +
228D ILE 5.0 0.2 - - - -
229D ASN* 3.9 13.7 - - - +
274D GLY 3.0 16.8 - - - +
275D MET* 3.2 10.7 - - - -
276D HIS* 3.0 24.6 + - + +
278D HIS* 2.9 16.8 + - - -
366D GLU* 3.0 2.9 - - - +
501D IQ1 4.0 11.2 - - + -
503D MG 2.1 27.4 - - - -
504D MG 1.9 33.0 - - - -
505D P3S 3.0 3.1 + - - -
506D PO4 3.4 7.6 - - - -
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Residues in contact with ALA 134 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D ALA 3.9 1.6 - - - -
133D GLU* 1.3 69.3 - - - +
135D GLU* 1.3 64.8 + - - +
136D PHE* 3.6 4.3 - - - -
226D ALA 4.7 0.2 - - - +
227D GLU* 5.2 1.6 - - - -
228D ILE 4.8 4.3 + - - +
230D TYR* 6.2 0.8 - - - -
242D MET* 3.6 24.5 - - + +
245D TYR* 2.9 48.3 + - + -
262D PHE* 3.9 5.6 - - + -
274D GLY 3.8 4.5 - - - -
275D MET* 4.5 2.0 - - + -
372D SER* 3.6 20.0 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il